Yes, they are all the same in terms of the command line. If your shells are in separate scans and you want to combine them, that can be done with the new beta version.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@icahn.mssm.edu>
Sent: Thursday, October 15, 2020 12:21 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] DTI scan process steps for single and multiple shells
 

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Hi Freesurfer experts,

Are the steps for processing DTI scan the same for single and multiple shells? for example, both via -prep, -bedp, -path. 
Thank you so much!

Best, 
Qi